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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 919/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSReg 1.40.0  (landing page)
Bahman Afsari , Elana J. Fertig
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/GSReg
git_branch: RELEASE_3_20
git_last_commit: 7fb6447
git_last_commit_date: 2024-10-29 09:53:18 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for GSReg on nebbiolo2

To the developers/maintainers of the GSReg package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GSReg.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GSReg
Version: 1.40.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GSReg.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GSReg_1.40.0.tar.gz
StartedAt: 2024-12-20 00:47:53 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 00:55:00 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 427.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GSReg.Rcheck
Warnings: 3

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GSReg.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GSReg_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GSReg.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GSReg/DESCRIPTION’ ... OK
* this is package ‘GSReg’ version ‘1.40.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GSReg’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘AnnotationDbi’ ‘GenomicFeatures’ ‘Homo.sapiens’ ‘org.Hs.eg.db’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GSReg.DIRAC.Pathways: no visible global function definition for ‘pnorm’
GSReg.DIRAC.mu: no visible global function definition for ‘var’
GSReg.Variance: no visible global function definition for ‘var’
GSReg.Variance: no visible global function definition for ‘pnorm’
GSReg.kendall.tau.distance.Restricted.Sparse.internal: no visible
  global function definition for ‘as’
GSReg.overlapJunction: no visible binding for global variable
  ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
GSReg.overlapJunction: no visible binding for global variable
  ‘org.Hs.eg.db’
GSReg.overlapJunction: no visible global function definition for
  ‘genes’
GSReg.overlapJunction: no visible global function definition for
  ‘mapIds’
GSReg.overlapJunction: no visible global function definition for
  ‘GRanges’
GSReg.overlapJunction: no visible global function definition for ‘Rle’
GSReg.overlapJunction: no visible global function definition for
  ‘IRanges’
GSReg.overlapJunction: no visible global function definition for
  ‘findOverlaps’
GSReg.overlapJunction: no visible global function definition for
  ‘queryHits’
GSReg.overlapJunction: no visible global function definition for
  ‘subjectHits’
GSReg.overlapJunction : <anonymous>: no visible global function
  definition for ‘findOverlaps’
GSReg.overlapJunction : <anonymous>: no visible global function
  definition for ‘Matrix’
GSReg.overlapJunction : <anonymous>: no visible global function
  definition for ‘queryHits’
GSReg.overlapJunction : <anonymous>: no visible global function
  definition for ‘subjectHits’
Undefined global functions or variables:
  GRanges IRanges Matrix Rle TxDb.Hsapiens.UCSC.hg19.knownGene as
  findOverlaps genes mapIds org.Hs.eg.db pnorm queryHits subjectHits
  var
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "pnorm", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) GSReg-package.Rd:20: Lost braces; missing escapes or markup?
    20 |   {B)  Calculate the DIRAC measure and p-value for it based on permutation test;}
       |   ^
checkRd: (-1) GSReg-package.Rd:22: Lost braces; missing escapes or markup?
    22 |   {C)  Calculate for a modified DIRAC method and a fast-efficient p-valuebased on U-Statistic theory;}
       |   ^
checkRd: (-1) GSReg-package.Rd:24: Lost braces; missing escapes or markup?
    24 |   {D)  Alternative Splicing Events in genes from a phenotype to other phenotype using their junction expression;}
       |   ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘GSReg.kendall.tau.distance.template’
Undocumented data sets:
  ‘geneExrsGSReg’ ‘junc.RPM.Simulated’ ‘phenotypes’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'GSReg_GeneSets_DIRAC.Rd':
GSReg.GeneSets.DIRAC
  Code: function(geneexpres, pathways, phenotypes, Nperm = 0, alpha =
                 0, minGeneNum = 5)
  Docs: function(geneexpres, pathways, phenotypes, Nperm = 0, alpha =
                 0.05, minGeneNum = 5)
  Mismatches in argument default values:
    Name: 'alpha' Code: 0 Docs: 0.05

Codoc mismatches from Rd file 'GSReg_GeneSets_VReg..Rd':
GSReg.GeneSets.EVA
  Code: function(geneexpres, pathways, phenotypes, verbose = T,
                 minGeneNum = 5, distFunc = GSReg.kendall.tau.distance,
                 distparamPathways, ...)
  Docs: function(geneexpres, pathways, phenotypes, minGeneNum = 5)
  Argument names in code not in docs:
    verbose distFunc distparamPathways ...
  Mismatches in argument names:
    Position: 4 Code: verbose Docs: minGeneNum

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in Rd file 'GSReg_Kendall.Rd':
  ‘GSReg.kendall.tau.distance.template’

Bad \usage lines found in Rd file 'GSReg_OverlapJunction.Rd':
   GSReg.overlapJunction <- function(juncExprs,
                                    GenestoStudy=NULL,
                                    geneexpr=NULL,
                                    minmeanloggeneexp= 3,
                                    alpha =0,
                                    sparse = F,
                                    genesCoordinatesTxDB = TxDb.Hsapiens.UCSC.hg19.knownGene, 
                                    geneIDInTxDB = 'ENTREZID', 
                                    geneIDOut = 'SYMBOL',
                                    org=org.Hs.eg.db, ...) 
Bad \usage lines found in Rd file 'GSReg_SEVA.Rd':
   function(juncExprs,
  		  phenoVect, 
            verbose=T,
            sparse =F, ...)

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... NOTE
The following files look like leftovers/mistakes:
  ‘Rplots.pdf’
Please remove them from your package.
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/GSReg.Rcheck/00check.log’
for details.


Installation output

GSReg.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL GSReg
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘GSReg’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c kendallTauDistance.cc -o kendallTauDistance.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c kendallTauDistanceFromTemp.cc -o kendallTauDistanceFromTemp.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c kendallTauDistanceRestricted.cc -o kendallTauDistanceRestricted.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c nij.cc -o nij.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c vect2compC.cc -o vect2compC.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o GSReg.so init.o kendallTauDistance.o kendallTauDistanceFromTemp.o kendallTauDistanceRestricted.o nij.o vect2compC.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-GSReg/00new/GSReg/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GSReg)

Tests output


Example timings

GSReg.Rcheck/GSReg-Ex.timings

nameusersystemelapsed
GSReg_GeneSets_DIRAC1.5490.0951.645
GSReg_GeneSets_VReg.0.9550.0200.974
GSReg_Kendall0.0030.0000.002
GSReg_OverlapJunction1.7200.0231.742
GSReg_SEVA2.3290.0772.406